Term
| Name a major function of the nucleus |
|
Definition
DNA replication
Gene transcription |
|
|
Term
| Name a major function of mitochondria |
|
Definition
|
|
Term
| Name a major function of chloroplasts |
|
Definition
|
|
Term
| Name a major function of ribosomes |
|
Definition
|
|
Term
| Name a function of the endoplasmic reticulum |
|
Definition
Modification of proteins
Synthesis of lipids
|
|
|
Term
| Name a function of the Golgi |
|
Definition
|
|
Term
| What class of lipid molecule is predominantly found in cellular membranes? |
|
Definition
|
|
Term
| Why are phospholipids polar while triglycerides are not polar? |
|
Definition
| Phospholipids have a phosphate group instead of one the of fatty acids |
|
|
Term
| What normally maitains the structure or integrity of cellular membranes? |
|
Definition
|
|
Term
| What does "the primary structure" of a protein refer to? |
|
Definition
|
|
Term
| Give an example of a post translational modification of a protein. |
|
Definition
Addition of carbohydrates
cleavage of pro protein
acetylation |
|
|
Term
| What are the three major groups for the common 20 amino acids found in proteins? |
|
Definition
Charged amino acids
Polar amino acids
Non-polar amino acids |
|
|
Term
| What type of bonds hold the two strands together in double stranded DNA? |
|
Definition
|
|
Term
| What is the most common way of separating the two strands (of DNA) in vitro? |
|
Definition
|
|
Term
| What type of molecule is produced in DNA replication? |
|
Definition
|
|
Term
| What type of molecule is produced in transcription? |
|
Definition
|
|
Term
| What type of molecule is produced in translation? |
|
Definition
|
|
Term
| A gene transcript is formed in the nucleus of a cell and moves to the cytoplasm where it is translated. What "processing" occurs during this movement? |
|
Definition
Caps 5' end with modified guanine
Adds poly A tail at 3' end
Splicing
|
|
|
Term
| Relative to the point where transcription begins, where would a gene promoter be found? |
|
Definition
| 10 or 35 base pairs upstream |
|
|
Term
| What molecule(s) bind to the promoter in order for transcription(gene expression) to occur? |
|
Definition
RNA Polymerase
transcription factors |
|
|
Term
| Are there more than, less than, or exactly 20 codons which code for the 20 amino acids found in proteins? |
|
Definition
|
|
Term
| What type of electophoresis is used to separate DNA molecules in automated procedures such as DNA sequencing and DNA profiling? |
|
Definition
| Capillary Electrophoresis |
|
|
Term
| What do Southern, Northern, and Western blots have in common? |
|
Definition
They separate, transfer molecules to different medium, and then detect the molecules on the new medium
Electrophoresis, transfer from gel to membrane, probing for specific molecule |
|
|
Term
| Of the three procedures (Southern, Northern, Western) which would be used to analyze DNA? |
|
Definition
|
|
Term
| What do restriction endonucleases do? |
|
Definition
| Cut within a sequence for a defined fragment |
|
|
Term
| A plasmid cloning vector requires an origin of replication. Why? |
|
Definition
| to be replicated in bacteria |
|
|
Term
| What other features are commonly found in plasmid cloning vectors? |
|
Definition
| Multiple cloning region, selection cassette (usually a gene producing antibiotic resistance), sequencing primer sequences flanking the cloning sites, blue/white screening, bacterial promoter for transcription of cloned inserted DNA |
|
|
Term
| When or for what purpose would a Yeast Artificial Chromosome(YAC) or Bacterial Artificial Chromosome(BAC) be used as a cloning vector? |
|
Definition
| When you have a very large sequence |
|
|
Term
|
Definition
| reverse transcription of mRNA |
|
|
Term
| A cDNA is a copy of what type of molecule? |
|
Definition
|
|
Term
| What would a cDNA library for normal human liver represent? |
|
Definition
| It would represent all the genes that were expressed in that tissue |
|
|
Term
| Why are thermo stable DNA polymerase used in the Polymerase Chain Reaction (PCR)? |
|
Definition
| To prevent destruction of the enzyme when heated during the denaturing step |
|
|
Term
| What components of the PCR mix are consumed during the amplification reactions and become part of the PCR product? |
|
Definition
|
|
Term
During the thermocycler program for a typical PCR might consist of:
94*C for 30 seconds-
55*C for 30 seconds-
72*C for 1 minute- |
|
Definition
94*C for 30 seconds- Denature DNA to separate strands
55*C for 30 seconds- Primers bind to DNA strands
72*C for 1 mintue- Polymerase synthesize new strands |
|
|
Term
| During a typical PCR reaction (thermocycler program), repeated 30 times during each of the 3 steps, what is happening? |
|
Definition
| Amplification of the DNA strand by an exponential amount |
|
|
Term
| What technique is used to determine if a specific gene is expressed in a tissue? |
|
Definition
| reverse transcriptase PCR |
|
|
Term
| What technique is used to determine quantitative differences between expression levels of a specific gene in different tissues? |
|
Definition
|
|
Term
| What technique is used to isolate the promoter for a specific gene (of known sequence) to clone into a plasmid as part of a transgene? |
|
Definition
|
|
Term
| What technique is used to determine the difference in expression of a large number of genes between normal tissue and a tumor from that tissue? |
|
Definition
|
|
Term
| What is used to analyze all of the proteins present in a tissue and determine unique proteins between different tissues? |
|
Definition
|
|
Term
| In the Sanger DNA sequencing reaction, what causes the termination of DNA synthesis? |
|
Definition
ddNTP
dideoxyribonucleotides |
|
|
Term
| In the 2D-electrophoresis of proteomics, proteins are separated by _____ in the first dimension and ____ in the second dimension. |
|
Definition
|
|
Term
| What information about the peptide fragments is determine by mass spectrometry in a proteomics experiment? |
|
Definition
|
|
Term
| In a typical two color DNA micro array protocol comparing two different tissues, what does it mean if a specific spot is yellow? |
|
Definition
| expressed in both tissues |
|
|
Term
| Describe an estrus synch protocol for cattle utilizing a progesteron releasing device such as a CIDR and PGF2alpha. |
|
Definition
day 0: insert CIDR
day 7: remove CIDR
day 6: PGF2alpha injection
day 8-10: estrus detection and AI
|
|
|
Term
| Describe a two injection prostaglandin estrus synch protocol. |
|
Definition
day 0: inject PGs(lutalyse)
Estrus detection and AI 2-5 days after
day 11: inject PGs
estrus detection and AI 2-5 days after
2 injections 11 days apart |
|
|
Term
| What is the "maternal to zygotic transition" in embryo development? |
|
Definition
| When the embryo stops relying upon transcripts stored in the oocyte and starts transcribing its own genome |
|
|
Term
| Why is compaction important in early embryo development? |
|
Definition
Intracellular connections formed/ Cell-Cell communication
|
|
|
Term
| When does oocyte activation occur? |
|
Definition
| When the sperm and oocyte membranes fuse at fertilization |
|
|
Term
Satellite DNA are small segments of DNA which are not part of the chromosomes and are located around the periphery of the the nucleus.
true or false? |
|
Definition
|
|
Term
|
Definition
| Single Nucleotide Polymorphism |
|
|
Term
Traits with low heritability or are difficult to measure are good candidates for Marker Assisted Selection.
True or False? |
|
Definition
|
|
Term
| What is a Quantitative Trait Loci or QTL? |
|
Definition
Location of a gene in a genome that has major economic effect.
A loci (region of the genome) where a gene (or genes) having major effects on a complex trait (one controlled by many genes) is located. |
|
|
Term
| What important transgenic technique (or type of experiment) is only possible with embryonic stem cells or nuclear transfer? |
|
Definition
| gene targeting (knock out or knock in) |
|
|
Term
| One method of making transgenic animals is to inject DNA into the nuclei of an early stage embryo. Where does the DNA used in such an injection come from? |
|
Definition
| Cloned DNA inserted in a plasmid and amplified by bacteria |
|
|
Term
| You would like to produce a transgenic animal which expresses a certain protein in its milk but not in other tissues. What would you include in the trangene to accomplish this goal? |
|
Definition
| tissue specific (mammary specific) promoter |
|
|
Term
| As a general rule does the inclusion of introns in a transgene increase or decrease expression of the transgene? |
|
Definition
|
|
Term
| When transgenic animals are made by pronuclear injection expression of the transgene will often vary between transgenic animals carrying the same transgene. Why? |
|
Definition
| Random position effects occur. Injection site is random and we don't know what the transgene will express. |
|
|
Term
| What is the cause of hyper acute rejection in xenotransplantation? |
|
Definition
| Natural circulating antibodies to the Gal epitope. When these antibodies recognize Gal on transplanted cells compliment is activated and the cells are destroyed |
|
|
Term
| In a transgene construct designed to create a "gene knock out" by homologous recombination, what is normally placed between the "arms of homology"? This is the segment of DNA that is inserted into the targeted gene during the homologous recombination reaction. |
|
Definition
selection cassette
Normally a gene which when expressed provides antibiotic resistance |
|
|
Term
| What is a tumor inducing (Ti) plasmid? Where does it come from and what is it used for? |
|
Definition
Plasmid from Agrobacterium which inserts a segment of DNA (T-DNA) into an infected plant and causes tumor growth.
The T-DNA of the native plasmid can be replaced with a transgene to create transgenic plants |
|
|
Term
| What is the major advantage of using particle bombardment in the production of transgenic plants? |
|
Definition
| unlimited range/ broad host range |
|
|
Term
| Describe two ways transgenic animals could potentially be important in human medicine. |
|
Definition
Serve as models for human diseases
Xenotransplantation
Production of drugs |
|
|
Term
| Give at least three components that could be included in a transgene construct (the DNA sequences that make up the transgene). |
|
Definition
Coding region
promoter
enhancer
poly adenylation sequence
insulator sequences |
|
|
Term
| Of the six broad classes of Genetically Engineered Animals described by the FDA based on their use, name or describe three. |
|
Definition
Enhance the quality of food
Improve animal health
Develop better animal interactions with humans
Produce products intended for human therapeutic use
Develop animal models for human diseases
Produce industrial or consumer products |
|
|
Term
| What is siRNA and how is it used? |
|
Definition
Small Interfering RNA
Reduce expression of specific genes by targeting the RISC to destroy that specific transcript. The RISC is targeted to the specific transcript by the sequence of the siRNA |
|
|
Term
| How can short hairpin RNA (shRNA) be used to impact or change gene expression? |
|
Definition
| shRNA can be inserted as a transgene and when expressed is converted to siRNA for long term suppression of gene expression |
|
|
Term
| What type of DNA sequences are commonly used in DNA profiling? |
|
Definition
|
|
Term
| What characteristic of microsatellites is highly variable between individuals? |
|
Definition
|
|
Term
| During fertilization, when does the acrosome reaction occur? |
|
Definition
| During penetration of the cumulus cell matrix, prior to penetration of the zona |
|
|
Term
| How do micro RNA's regulate gene expression? |
|
Definition
| Post transcriptional regulation/ inhibit translation |
|
|
Term
| How are viral vector made to be Replication Defective? |
|
Definition
| Incorporation of the genes required to make an infective viral particle on separate plasmids other than the plasmid containing the actual viral vector. All plasmids are transfected into a packaging cell which assembles an infective viral particle. |
|
|
Term
| How has the bovine embryo transfer industry changed during the last 5 years? |
|
Definition
Emergence of S. America as a major market
Increased significance of cryopreserved embryos
Increased use of IVP embryos |
|
|
Term
| If a donor cow is superovulated during a natural cycle (no estrus synch) approximately what day of the cycle should FSH injections start? |
|
Definition
|
|
Term
| If a large number of cows are superovulated with FSH approximately how many total ova will be collected (ave per cow)? |
|
Definition
|
|
Term
| Approximately how many viable embryos will be collected (ave per cow) when a large group of cows are super ovulated? |
|
Definition
|
|
Term
| If all of the viable embryos are transferred to recipients without cryopreservation, approximately how many pregnancies will result (ave per cow)? |
|
Definition
|
|
Term
| If there is a dominant follicle present on one ovary of a cow on the day FSH injections are started, would you expect the superovulation to be highly successful? Why? |
|
Definition
No
The dominant follicle will have caused the smaller follicles to begin to regress. It is unlikely that FSH would be able to rescue these follicles. |
|
|
Term
| If super ovulated donor cattle are collected non-surgically 7 days after estrus what stage(s) of embryos would you expect to recover? |
|
Definition
|
|
Term
| When bovine embryos are transferred non-surgically to a recipient, which side of the reproductive tract (which uterine horn) should they be transferred to? |
|
Definition
Ipsi lateral
Same side as the CL |
|
|
Term
| If bovine embryos are transferred into recipients that were 24 hours before the super ovulated donor cow they were collected from, you would expect the pregnancy rate to be higher, lower, or about the same compared to transfer into recipients that were in estrus at the same time as the donor? All factors except the synchrony are equivalent. |
|
Definition
|
|
Term
| What factors can change the pregnancy rate of the recepient cow when it is +/- 24 hours off from the donor cow? |
|
Definition
Recipient management:
nutrition
health
stress
accuracy of estrus detection
technician skills |
|
|
Term
| In Vitro embryo production (IVP) consists of three separate components, what are they? |
|
Definition
|
|
Term
| Immature oocytes aspirated from follicles must be surounded by what kind of cells in order to produce a high quality mature oocyte after in vitro maturation? |
|
Definition
|
|
Term
| What role does heparin play in a bovine in vitro fertilization system? |
|
Definition
|
|
Term
| For bovine in vitro fertilization using frozen semen, how would you produce a highly motile sperm preparation to use for fertilization? |
|
Definition
Percol density gradient
swim-up |
|
|
Term
| Give two applications of bovine IVP in commercial cattle production. |
|
Definition
Embryos donors that do not respond to superovulation
Embryos from pregnant cattle
Producing large number of embyros in short period of time
F1 cattle for dairy production
Dairy replacement heifers in beef cattle |
|
|
Term
| Give an example of a penetrating cryoprotectant. |
|
Definition
DMSO
glycerol
ethylene glycol |
|
|
Term
| Give an example of a non penetrating cryoprotectant. |
|
Definition
Sucrose
glucose
trelulose |
|
|
Term
| During the addition and removal of a penetrating cryoprotectant what is the potential problem which could reduce survival if not controlled? |
|
Definition
| Water moves across the cell membranes faster than cryoprotectant. Can cause shrinkage during cryoprotectant addition or swelling during cryoprotectant removal. |
|
|
Term
| This problem is greatest during removal of a penetrating cryoprotectant. Give three ways this problem has been controlled in the cryopreservation of bovine embryos. |
|
Definition
Stepwise removal
Use of sucrose or other non penetrating cryoprotectant
Use of ethylene glycol as the cryoprotectant |
|
|
Term
| Why is the cooling rate controlled in a conventional embryo cryopreservation procedure? |
|
Definition
| Prevention of ice crystal formation inside the cells. Ice crystals form outside the cells and grow by drawing water from inside the cells. Cooling rate must be controlled in order to allow time for the water to leave the cells. |
|
|
Term
| What method of embryo sexing has been reliable and has had limited commercial application in the bovine embryo transfer industry? |
|
Definition
| PCR amplification of y specific DNA sequences |
|
|
Term
| The semen sexing procedure described in class is based on what property? |
|
Definition
| X chromosome is larger than the Y chromosome, larger amount of DNA |
|
|
Term
| What has been the major technical problem with application of this technology for artificial insemination? |
|
Definition
| Sorting speed makes it difficult to have enough sorted semen for conventional AI doses |
|
|
Term
| What procedure utilizing sexed semen can be used to solve this problem? |
|
Definition
|
|
Term
| What is the most common method used today for synchronizing estrus in pigs? |
|
Definition
| Feeding of Altrenogest, Matrix |
|
|
Term
| What is the major difference between embryo collection and transfer in sheep, goats and pigs compared to the same procedures in cattle? |
|
Definition
| Surgical vs. non surgical collection and transfer |
|
|
Term
| The early experiments with nuclear transfer were conducted with what species? |
|
Definition
|
|
Term
| How did the procedure used to clone Dolly differ from the procedures used to clone mammals (including domestic animals) prior to that? |
|
Definition
| Use of somatic cells from adult animals. Prior to that mammals were cloned by nuclear transfer using embryonic cells |
|
|
Term
| From what cells are embryonic stem cells derived? |
|
Definition
|
|
Term
| Name two tissues from which human adult stem cells have been isolated. |
|
Definition
Bone marrow
cord blood
fat
skin
muscle
central nervous system |
|
|
Term
| What are induced pluripotent stem (iPS) cells? |
|
Definition
| Differentiated somatic cells induced to be pluripotent and very much like embryonic stem cells. Most commonly done by transfection with viral vectors expressing pluripotency genes (transcription factors) such as Oct 4, Nanog and Sox 2 |
|
|
Term
| Why are human induced pluripotent stem cells considered to be much better for use in tissue regeneration applications compared to human embryonic stem cells? |
|
Definition
| Cells very much like embryonic stem cells can be induced without the need to destroy an embryo or create an embryo for this purpose |
|
|
Term
With embryo splitting fewer pregnancies are produced per embryo collected but the procedure can produce identical twins which are much more valuable so the procedure is frequently used in the bovine embryo transfer industry.
true or false? |
|
Definition
|
|
Term
Laser cutting of the zona pellucida for assisted hatching is frequently applied during embryo transfer in domestic animals but very seldom used in ART procedures.
true or false? |
|
Definition
|
|
Term
Sheep, goats and horses are seasonal breeders.
true or false? |
|
Definition
|
|
Term
Embryos are easily recovered from the uterus of the pig with a non surgical procedure.
true or false? |
|
Definition
|
|
Term
Super ovulation in mares can be expected to yield a similar number of embryos as is expected from super ovulation in cattle.
true or false? |
|
Definition
|
|
Term
Cryopreservation of equine embryos is common and highly successful.
true or false? |
|
Definition
|
|
Term
Somatic cell nuclear transfer has been successful in many mammalian species including domestic laboratory and companion animals.
true or false? |
|
Definition
|
|
Term
| When is a woman/man considered infertile? |
|
Definition
| 12 months of unprotected intercourse without pregnancy |
|
|
Term
| What are some treatments of infertility? |
|
Definition
- Insemination
- ovarian stimulation/insemination
- in vitro fertilization
- intracytoplasmic sperm injection (ICSI)
- assisted hatching
- other (non ART) approaches
|
|
|
Term
| Which treatment of infertility has the most controversy and would most likely be skipped? Why? |
|
Definition
Ovarian stimulation
Very little control because it can cause multiple births |
|
|
Term
| Hormone of choice for ovarian stimulation.. |
|
Definition
|
|
Term
| Why would multiple births be the greatest risk of ovarian stimulation? |
|
Definition
Greatest in young women
Significant risk to mother(preclamsia) and children
huge cost to medical system |
|
|
Term
| What are the steps of IVF? |
|
Definition
Ovarian Stimulation
Aspirate from ovary
Mix sperm and eggs
Culture
Uterine transfer |
|
|
Term
| In IVF, how long are the eggs cultured and on what day are they transferred? What is the issue with transferring on this day? |
|
Definition
Cultured for 2 days, 4-8 cell stage
transferred on day 3
Because cells are cultured for a short period of time many embryos can be transferred before maternal to zygotic transition (not uterine stage). Not selecting for embryos. This is why there's the risk of multiple births, quantity over quality |
|
|
Term
| When would be a better day to transfer cultured embryos? Why? |
|
Definition
day 5 when they are blastocyst stage
Cultured longer and transferred at the blastocyst stage (uterin stage) so that only need to transfer one embryo instead of many to increase the probability of pregnancy. Quality over quantity |
|
|
Term
| How long can a typical IVF treatment take? |
|
Definition
| 22-24 days depending on how long the eggs are cultured |
|
|
Term
|
Definition
Intracytoplasmic Sperm Injection
Direct injection of sperm instead of IVF |
|
|
Term
| When is ICSI usually used? |
|
Definition
| male associated infertility |
|
|
Term
|
Definition
| Primplantation Genetic Diagnosis |
|
|
Term
| What are the clinical indications of PGD? |
|
Definition
- Single gene defects
- balanced translocations
- recurrent pregnancy loss
- advanced maternal age
- repetitive IVF failure
- embryo selection
|
|
|
Term
| What is an embryo that doesn't have the full set (24) of chromosomes? |
|
Definition
|
|
Term
| When should an embryo biopsy be done? Why? |
|
Definition
prior to 67 hours post retrieval
Implantation rates significantly lower if after 70 hours |
|
|
Term
| What is the Minitube Bovine Sex-Y kit used for? |
|
Definition
|
|
Term
| In the Minitube Bovine Sex-Y kit, what does it mean when there is a bright red fluorescent signal? |
|
Definition
| indicates a Y chromosome within the nuclear DNA |
|
|
Term
| Polar bodies can be used to determine ____ |
|
Definition
| the genetic component of the cells |
|
|
Term
| What MUST be done before any clinical studies can be requested? |
|
Definition
|
|
Term
| What is the first step of human drug approval and what is usually done? |
|
Definition
Pre Clinical Research:
Gene expression studies
cell culture
animal studies
manufacture, purification |
|
|
Term
| What is the second step of human drug approval? |
|
Definition
Phase One:
Safety- will person survive? |
|
|
Term
| What is the third step of human drug approval? |
|
Definition
Phase Two:
Safety and dose plus efficacy- tested on those drug is meant for |
|
|
Term
| What is the fourth step of human drug approval? |
|
Definition
Phase Three:
Efficacy- dose should be established and safety should be established |
|
|
Term
| What happens after the fourth step in human drug approval? |
|
Definition
| Will go into a larger study and will begin treating a larger base |
|
|
Term
| What is RAC and what did it do? |
|
Definition
Recombinant DNA Advisory Committee
Est. biological and physical confinement levels
Classified organisms by probability of surviving in the environment |
|
|
